There are two areas of the game that should be addressed, logic errors and historical errors.
Historical errors can be debated and if simplicity and/or time to fix are too great, then I am fine with that. Disapointed but can understand the decision. Logical errors on the other hand totally ruin the game (at least for me) and should be fixed if at all possible.
Supply - Enemy units out of supply regenerating in cities
Amphs and AKs - can build as many as you have PP for in a week
Naval routines - Amphs, Convoys, and AKs ignored by opposing warships. As a side note, unless the escorting side has a much greater number of ships (i.e. DDay) there should be no way a small fleet (i.e. German) should prevent these type of ships from combat loses
Instant transfer of units - Units in territory that surrenders are put into the deployment pool. They can then be placed anywhere on the map. So in a week you could go from the bowels of France to the Eastrn front. Or in my case, from Northern England to the Eastern From in a week. Considering it takes three weeks to be able to move and attack with a unit overseas, this is not right. (Load a unit on an AK and move to sea week 1, move to port and unload, can't move week 2, can move and attack week 3)
Russia declaring war in 1940 - fixed in a hot patch I understand
Britian being puppeted or surendering - Puppeting should not be allowed at all imho. Not even sure if they should surrender either as they had plenty of choices of where to move the government to. So I would allow Germany to control the captured cites in GB (so they can get PPs for them), but I would NOT allow them to be able to deploy units there.
Findland and Leningrad - Have not confirmed this, but the Fins honored their treaty with Russia to not attack Leningrad. So in the game the Fins should not be allowed to attack the city.
No British fleet protecting England
No cooridinated attacks against land units by allies - At least I have not found a way to do it
Winter of 1941 in Russia. - Not sure if this is modeled, but indications are that it is not. If it is modeled, then it should ONLY apply if the Germans attack Russia in 1941. If they attack at any other time then the effects should not apply.
Rail Repair in Russia - Seems to be way too generous considering different guages were used. Also supply in Russia seems to be way to easy as well.
Please, please add a summary screen at the start of each turn
I would complete remove any requirement that the player has to keep moving their ships to port for refit. For me it is constant pain to have to look at the naval report, determing who should return to port, then next turn send them back to sea. It totally ruins the flow of the game for me. I would just assume that this is going on and not force the player to have to deal with this level of control when in so many other areas of the game you do not require this level of micromanagement.